FIMO: Scanning for occurrences of a given motif

Charles E. Grant, Timothy L. Bailey and William Stafford
Noble

Bioinformatics. 27(7):1017-1018, 2011.

Abstract

A motif is a short DNA or protein sequence that contributes to the
biological function of the sequence in which it resides. Over the past
several decades, many computational methods have been described for
identifying, characterizing and searching with sequence
motifs. Critical to nearly any motif-based sequence analysis pipeline
is the ability to scan a sequence database for occurrences of a given
motif described by a position-specific frequency matrix.

We describe Find Individual Motif Occurrences (FIMO), a software tool
for scanning DNA or protein sequences with motifs described as
position-specific scoring matrices. The program computes a
log-likelihood ratio score for each position in a given sequence
database, uses established dynamic programming methods to convert this
score to a P-value and then applies false discovery rate analysis to
estimate a q-value for each position in the given sequence. FIMO
provides output in a variety of formats, including HTML, XML and
several Santa Cruz Genome Browser formats. The program is efficient,
allowing for the scanning of DNA sequences at a rate of 3.5 Mb/s on a
single CPU.

FIMO is part of the MEME Suite software toolkit. A web server and
source code are available
at http://meme.sdsc.edu.